def numCopies(self, allele): """Return the number of copies of the allele.""" if type(allele) == str: allele = Allele.get(allele.upper()) if type(allele) != Allele: raise Exception, "Must supply Allele or allele abbreviation." chromo = allele.onChromo cnt = 0 # Autosomal if chromo in [2, 3, 4]: if allele in self.chromos[0][chromo-1]: cnt += 1 if allele in self.chromos[1][chromo-1]: cnt += 1 return cnt # Sex-linked if allele in self.chromos[0][0]: cnt += 1 if not self.isFemale(): return cnt if allele in self.chromos[0][1]: cnt += 1 return cnt
def isDead(self): """The individual is dead if it has any two lethal allele copies.""" lethals = Allele.getLethals() for al in lethals: num = self.numCopies(al) if num > 1: return True # Hemizygous males if type(al.onChromo) == str and num > 0 and not self.isFemale(): return True return False
def setAs(self, allele): """Set HOMOZYGOUS for the allele, unless lethal or sex-linked. Supply the allele abbreviation for lookup. Returns False if the allele couldn't be set (x-linked lethal for males.) """ if type(allele) == str: allele = Allele.get(allele.upper()) if type(allele) != Allele: raise Exception, "Must supply allele or allele abbreviation." if self.numCopies(allele) > 0: raise Exception, "Cannot set allele if already present." chromo = allele.onChromo lethal = allele.isLethal() if chromo not in [2, 3, 4, 'x', 'X']: raise Exception, \ "Allele supplied is not on a valid chromosome." # Autosomal genes if chromo in [2, 3, 4]: self.chromos[0][chromo-1].append(allele) if not lethal: self.chromos[1][chromo-1].append(allele) return # X-linked genes if not self.sex: self.__cacheSex() # Can't manually create X-linked lethal males! if self.sex == 'm' and lethal: return self.chromos[0][0].append(allele) if self.sex == 'f' and not lethal: self.chromos[1][0].append(allele) return
